2013 |
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Revues avec comité de lecture |
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A. Lorenz, and Y. Ponty
Non-redundant random generation algorithms for weighted context-free languages
Theoretical Computer Science, To appear, 2013 [pdf] [hal]
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Y. Zhang, Y. Ponty, M. Blanchette, E. Lecuyer, and J. Waldispühl
SPARCS: a web server to analyze (un)structured regions in coding RNA sequences
Nucleic Acids Research, To appear 2013 [pdf] [hal]
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Conférences avec comité de lecture et actes |
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V. Reinharz, Y. Ponty, and J. Waldispühl
A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotides distribution
Proceedings of ISMB/ECCB - 21st Annual international conference on Intelligent Systems for Molecular Biology/12th European Conference on Computational Biology - 2013, Allemagne, 2013 [pdf] [hal]
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V. Reinharz, Y. Ponty, and J. Waldispühl
A linear inside-outside algorithm for correcting sequencing errors in structured RNA sequences
Proceedings of RECOMB - 17th Annual International Conference on Research in Computational Molecular Biology - 2013, Chine, 2013 [pdf] [hal]
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E. Senter, S. Sheikh, I. Dotu, Y. Ponty, and P. Clote
Using the Fast Fourier Transform to accelerate the computational search for RNA conformational switches (extended abstract)
Proceedings of RECOMB - 17th Annual International Conference on Research in Computational Molecular Biology - 2013, Chine, 2013 [pdf] [hal]
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Divers/Soumis |
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Y. Zhou, Y. Ponty, S. Vialette, J. Waldispühl, Y. Zhang, and A. Denise
Flexible RNA design under structure and sequence constraints using formal languages
[pdf] [hal]
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2012 |
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Revues avec comité de lecture |
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P. Clote, Y. Ponty, and J.-M. Steyaert
Expected distance between terminal nucleotides of RNA secondary structures.
Journal of Mathematical Biology, 65(3):581-99, 2012 [doi] [pdf] [hal] [pubmed]
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E. Senter, S. Sheikh, I. Dotu, Y. Ponty, and P. Clote
Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches
PLoS ONE, 7(12):e50506, 2012 [doi] [hal]
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A. Levin, M. Lis, Y. Ponty, C. O'Donnell, S. Devadas, B. Berger, and J. Waldispühl
A global sampling approach to designing and reengineering RNA secondary structures.
Nucleic Acids Research, 40(20):10041-52, 2012 [doi] [hal] [pubmed]
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Conférences avec comité de lecture et actes |
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J. Du Boisberranger, D. Gardy, and Y. Ponty
The weighted words collector
Proceedings of AOFA - 23rd International Meeting on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms - 2012, Canada, dmAQ01243--264, 2012 [pdf] [hal]
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S. Sheikh, R. Backofen, and Y. Ponty
Impact Of The Energy Model On The Complexity Of RNA Folding With Pseudoknots
Proceedings of CPM - 23rd Annual Symposium on Combinatorial Pattern Matching - 2012, Finlande, 7354321--333, 2012 [doi] [pdf] [hal]
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C. Banderier, O. Bodini, Y. Ponty, and H. Tafat
On the diversity of pattern distributions in combinatorial systems
Proceedings of ANALCO - 12th Meeting on Analytic Algorithmics and Combinatorics - 2012, Japon, 107--116, 2012 [pdf] [hal]
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P. Rinaudo, Y. Ponty, D. Barth, and A. Denise
Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots
Proceedings of WABI - 12th Workshop on Algorithms in Bioinformatics - 2012, Slovénie, 2012 [pdf] [hal]
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S. Janssen, L. Paulevé, Y. Ponty, B. Raman, and M. Zytnicki
Can Probabilistic Model Checking Explore Ribo-Nucleic Acid Folding Space?
Proceedings of IWBDA - 4th International Workshop on Bio-Design Automation - 2012, États-Unis, 2012 [hal]
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Exposés invités |
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Y. Ponty
Visualizing 2D & 3D Structures of RNA
Proceedings of VIZBI - 3rd international meeting on Visualizing Biological Data - 2012, Allemagne, 2012 [hal]
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J. Waldispühl, B. Berger, S. Devadas, P. Clote, and Y. Ponty
Efficient Algorithms to Explore the RNA Mutational Landscape
Proceedings of DM - SIAM Conference on Discrete Mathematics - 2012, Canada, 2012 [hal]
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Divers/Soumis |
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Y. Ponty
Rule-weighted and terminal-weighted context-free grammars have identical expressivity
[pdf] [hal]
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2011 |
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Revues avec comité de lecture |
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J. Waldispühl, and Y. Ponty
An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure.
Journal of Computational Biology, 18(11):1465-79, 2011 [doi] [hal] [pubmed]
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Conférences avec comité de lecture et actes |
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J. Waldispühl, and Y. Ponty
An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure
Proceedings of RECOMB - 15th Annual International Conference on Research in Computational Molecular Biology - 2011, Canada, 6577501-515, 2011 [doi] [pdf] [hal]
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Y. Ponty, and C. Saule
A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms
Proceedings of WABI - 11th Workshop on Algorithms in Bioinformatics - 2011, Allemagne, 2011 [pdf] [hal]
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Conférences avec comité de lecture |
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S. Janssen, Y. Ponty, B. Raman, S. Sheikh, J.-M. Steyaert, and P. Clote
Investigating the RFAM paradox: The pseudoknot explanation
Proceedings of Fifth Indo-French Bioinformatics Meeting, Inde, 2011 [pdf] [hal]
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2010 |
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Revues avec comité de lecture |
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A. Denise, Y. Ponty, and M. Termier
Controlled non uniform random generation of decomposable structures
Theoretical Computer Science, 411(40-42):3527-3552, 2010 [doi] [pdf] [hal]
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Conférences avec comité de lecture et actes |
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D. Gardy, and Y. Ponty
Weighted random generation of context-free languages: Analysis of collisions in random urn occupancy models
Proceedings of GASCOM - 8th conference on random generation of combinatorial structures - 2010, Canada, 14pp, 2010 [pdf] [hal]
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O. Bodini, and Y. Ponty
Multi-dimensional Boltzmann Sampling of Languages
Proceedings of AOFA - 21st International Meeting on Probabilistic, Combinatorial, and Asymptotic Methods in the Analysis of Algorithms - 2010, Autriche, 49--64, 2010 [pdf] [hal]
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2009 |
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Revues avec comité de lecture |
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K. Darty, A. Denise, and Y. Ponty
VARNA: Interactive drawing and editing of the RNA secondary structure.
Bioinformatics, 25(15):1974-5, 2009 [doi] [pdf] [hal] [pubmed]
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2008 |
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Revues avec comité de lecture |
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Y. Ponty
Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy: The boustrophedon method
Journal of Mathematical Biology, 56(1-2):107--127, 2008 [doi] [hal]
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M. Bousquet-Mélou, and Y. Ponty
Culminating paths
Discrete Mathematics and Theoretical Computer Science, 10(2):125--152, 2008 [pdf] [hal]
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W. Lorenz, P. Clote, and Y. Ponty
Asymptotics of RNA shapes
Journal of Computational Biology, 15(1):31--63, 2008 [doi] [hal]
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Y. Ponty, R. Istrate, E. Porcelli, and P. Clote
LocalMove: computing on-lattice fits for biopolymers
Nucleic Acids Research, 36(2):W216-W222, 2008 [doi] [hal]
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Conférences avec comité de lecture et actes |
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Y. Ponty
Non-redundant random generation from weighted context-free languages
Proceedings of GASCOM - 7th conference on random generation of combinatorial structures - 2008, Italie, 12pp, 2008 [pdf] [hal]
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2007 |
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Revues avec comité de lecture |
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F. Fabrizzio, Y. Ponty, W. Lorenz, and P. Clote
DIAL: A web server for the pairwise alignment of two RNA 3-dimensional structures using nucleotide, dihedral angle and base pairing similarities
Nucleic Acids Research, 35(Web server issue):W659--668, 2007 [doi] [hal]
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2006 |
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Revues avec comité de lecture |
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Y. Ponty, M. Termier, and A. Denise
GenRGenS: Software for Generating Random Genomic Sequences and Structures
Bioinformatics, 22(12):1534--1535, 2006 [doi] [pdf] [hal]
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Thèses |
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Y. Ponty
Modélisation de séquences génomiques structurées, génération aléatoire et applications
[Université Paris Sud - Paris XI], 2006 [pdf] [hal]
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2004 |
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Conférences avec comité de lecture et actes |
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G. Kucherov, L. Noé, and Y. Ponty
Estimating seed sensitivity on homogeneous alignments
Proceedings of 4th Symposium on Bioinformatics and bioengineering - BIBE'2004, Taïwan, Province De Chine, 387-394, 2004 [doi] [pdf] [hal]
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2003 |
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Rapports |
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G. Kucherov, L. Noé, and Y. Ponty
Estimating seed sensitivity on homogeneous alignments
Rapport de recherche RR-5047, 2003 [pdf] [hal]
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